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Old 04-27-2014, 04:06 AM   #1
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 193
Exclamation Hands-On Training in Discovering Standard and Non-standard Transcripts



Discovering standard and non-standard RNA transcripts
How to detect canonical splicing, circular RNAs, trans-splicing, and fusion transcripts



When?
October 23rd - 24th 2014

Where?
Leipzig, Germany


Scope and Topics

The purpose of this workshop is to get a deeper understanding in the usage of split-read mapping in order to find splice junctions, predict new isoforms and uncover non-standard RNA molecules, like circularized RNAs or fusion-transcripts. Advantages and disadvantages of the so-called split-reads and their implications on data analyses will be covered. The participants will be trained to understand the mapping approach, to find potential problems/errors and finally to implement their own pipelines. After this course they will be able to find and analyze (non-) standard exon-exon junctions and create ready-to-use analyses pipelines.

By the end of this workshop the participants will:
  • understand the implications of splicing or fusion events and the concept of split-reads
  • understand how to detect splice sites using split-read information
  • know how to predict and quantify different isoforms of genes
  • be able to find circularized RNAs or fusion-stranscripts
  • be able to perform differential splicing analyis
  • automate tasks with shell scripting to create reusable data pipelines
  • plot and visualize results
  • be able to reuse all analyses

Requirements
  • basic linux knowledge (shell usage, common commands). You should be familiar with the commands covered in the Learning the Shell Tutorial
  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • knowledge in standard HTS analyses and data formats (FASTQ, SAM, samtools, ...)

Target Audience
  • biologists or data analysts with some experience in analyzing HTS data

Included in Course
  • Course materials
  • Catering
  • Conference Dinner

Program

To be announced...

Speakers

Gero Doose (University of Leipzig) found and published several circularized RNAs in various RNA-Seq experiments. He specialized on split-read analysis some years ago and has a strong expertise in downstream analyses.

Christian Otto (University of Leipzig) is one of the developers of the split-read mapping tool segemehl and is an expert on implementing efficient algorithms for HTS data analyses.

David Langenberger (ecSeq Bioinformatics) started working with small non-coding RNAs in 2006. Since 2009 he specialized on NGS technolgies. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC).

Guest-speaker:
Invited speaker (Pacific Biosciences) will give a short presentation about the benefits of ultra-long reads in isoform detection.

Key Dates

Opening Date of Registration: April 1st 2014
Closing Date of Registration: August 1st 2014
Workshop: October 23rd-24th 2014 (8:00 - 17:00)

Attendance

Location: Leipzig, Germany.
Language: English
Available seats: 20 (first-come, first-served)

Registration fees:

industry rate: 850 EUR
academic rate: 600 EUR
Travel expenses and accommodation are not covered by the registration fee.

Note: Combine this workshop with our other workshops and get 10% discount.

Contact

ecSeq Bioinformatics
Brandvorwerkstr.43
04275 Leipzig
Germany
Email: [email protected]

Downloads

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When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.


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Find more information at http://www.ecseq.com/workshops/workshop_2014-04.html
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

Last edited by ecSeq Bioinformatics; 07-15-2014 at 06:28 AM.
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Old 07-15-2014, 06:31 AM   #2
ecSeq Bioinformatics
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Location: Leipzig, Germany

Join Date: May 2012
Posts: 193
Default

I am very excited to announce that Pacific Biosciences decided to sponsor this course and send a speaker to give a short presentation, highlighting the benefits of ultra-long reads in isoform detection.

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